Package net.sf.mzmine.util

Examples of net.sf.mzmine.util.Range

52
53
54
55
56
57
58
59
60
61
62
    HistogramDataType dataType = parameters.getParameter(
        HistogramParameters.dataRange).getType();
    int numOfBins = parameters.getParameter(HistogramParameters.numOfBins)
        .getValue();
    Range range = parameters.getParameter(HistogramParameters.dataRange)
        .getValue();

    setDefaultCloseOperation(DISPOSE_ON_CLOSE);
    setBackground(Color.white);
View Full Code Here
119
120
121
122
123
124
125
126
    String minText = minNodes.item(0).getTextContent();
    String maxText = maxNodes.item(0).getTextContent();
    double min = Double.valueOf(minText);
    double max = Double.valueOf(maxText);
    value = new Range(min, max);

  }
View Full Code Here
65
66
67
68
69
70
71
72
73
74
75
76
77
      return ExitCode.ERROR;
    }

    int msLevel = parameters.getParameter(TwoDParameters.msLevel)
        .getValue();
    Range rtRange = parameters.getParameter(
        TwoDParameters.retentionTimeRange).getValue();
    Range mzRange = parameters.getParameter(TwoDParameters.mzRange)
        .getValue();
    TwoDVisualizerWindow newWindow = new TwoDVisualizerWindow(dataFiles[0],
        msLevel, rtRange, mzRange, parameters);

    MZmineCore.getDesktop().addInternalFrame(newWindow);
View Full Code Here
174
175
176
177
178
179
180
181
182
183
184
    Scan fragmentScan = dataFile.getScan(fragmentScanNumber);
    if (fragmentScan == null)
      return false;

    // Get MS/MS data points in the tolerance range
    Range ms2mzRange = ms2mzTolerance.getToleranceRange(possibleFragment
        .getAverageMZ());

    DataPoint fragmentDataPoints[] = fragmentScan
        .getDataPointsByMass(ms2mzRange);
View Full Code Here
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
    SimplePeakList newList = new SimplePeakList(selectedPeakList.getName(),
        selectedPeakList.getRawDataFiles());

    Vector<PeakListRow> peakRows = new Vector<PeakListRow>();

    Range mzRange = selectedPeakList.getRowsMZRange();
    Range rtRange = selectedPeakList.getRowsRTRange();

    PeakThresholdMode selectedPeakOption = (PeakThresholdMode) thresholdCombo
        .getSelectedItem();
    if (selectedPeakOption == PeakThresholdMode.TOP_PEAKS_AREA) {
      mzRange = masterFrame.getPlot().getXYPlot().getAxisRange();
      rtRange = masterFrame.getPlot().getXYPlot().getDomainRange();
    }

    for (PeakListRow peakRow : selectedPeakList.getRows()) {
      if (mzRange.contains(peakRow.getAverageMZ())
          && rtRange.contains(peakRow.getAverageRT())) {
        peakRows.add(peakRow);
      }
    }

    Collections.sort(peakRows, new PeakListRowSorter(
View Full Code Here
109
110
111
112
113
114
115
116
117
118
119
120
        double pointRTMin = imageRTMin + (i * imageRTStep);
        double pointRTMax = pointRTMin + imageRTStep;
        double pointMZMin = imageMZMin + (j * imageMZStep);
        double pointMZMax = pointMZMin + imageMZStep;

        values[i][j] = dataset.getMaxIntensity(new Range(pointRTMin,
            pointRTMax), new Range(pointMZMin, pointMZMax),
            plotMode);

        if (values[i][j] > maxValue)
          maxValue = values[i][j];

View Full Code Here
161
162
163
164
165
166
167
168
    return true;

  }

  Range getDomainRange() {
    return new Range(getDomainAxis().getRange().getLowerBound(),
        getDomainAxis().getRange().getUpperBound());
  }
View Full Code Here
166
167
168
169
170
171
172
173
    return new Range(getDomainAxis().getRange().getLowerBound(),
        getDomainAxis().getRange().getUpperBound());
  }

  Range getAxisRange() {
    return new Range(getRangeAxis().getRange().getLowerBound(),
        getRangeAxis().getRange().getUpperBound());
  }
View Full Code Here
80
81
82
83
84
85
86
87
88
89
   */
  public Chromatogram(RawDataFile dataFile) {
    this.dataFile = dataFile;

    // Create a copy, not a reference
    rawDataPointsRTRange = new Range(dataFile.getDataRTRange(1));

    dataPointsMap = new Hashtable<Integer, DataPoint>();
    buildingSegment = new Vector<Integer>(128);
  }
View Full Code Here
212
213
214
215
216
217
218
219
220
221
222
223
      // don't need the additional data provided by the MzPeak

      dataPointsMap.put(allScanNumbers[i], mzPeak);

      if (i == 0) {
        rawDataPointsIntensityRange = new Range(mzPeak.getIntensity());
        rawDataPointsMZRange = new Range(mzPeak.getMZ());
      } else {
        rawDataPointsIntensityRange.extendRange(mzPeak.getIntensity());
        rawDataPointsMZRange.extendRange(mzPeak.getMZ());
      }
View Full Code Here
TOP

Related Classes of net.sf.mzmine.util.Range

  • net.sf.mzmine.data.impl.SimpleChromatographicPeak
  • net.sf.mzmine.data.impl.SimplePeakList
  • net.sf.mzmine.data.impl.SimpleScan
  • net.sf.mzmine.modules.deconvolutedanalysis.CorrectedSpectrum
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameAlignmentProcessingTask
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.FameCorrection
  • net.sf.mzmine.modules.deconvolutedanalysis.famealignment.table.ResultsListTable
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.MassCandidate
  • net.sf.mzmine.modules.deconvolutedanalysis.massdetection.SpectraMatcherComparisonTask
  • net.sf.mzmine.modules.deconvolutedanalysis.spectrafilter.SpectraFilterTest
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.